HEADER HYDROLASE 19-MAY-11 2YJ8 TITLE CATHEPSIN L WITH A NITRILE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATHEPSIN L1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 114-333; COMPND 5 SYNONYM: MAJOR EXCRETED PROTEIN, MEP, CATHEPSIN L1 HEAVY CHAIN, COMPND 6 CATHEPSIN L1 LIGHT CHAIN; COMPND 7 EC: 3.4.22.15; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE, DRUG DESIGN, THIOL PROTEASE EXPDTA X-RAY DIFFRACTION AUTHOR D.W.BANNER,J.M.BENZ,W.HAAP REVDAT 2 06-NOV-24 2YJ8 1 REMARK LINK REVDAT 1 23-NOV-11 2YJ8 0 JRNL AUTH L.A.HARDEGGER,B.KUHN,B.SPINNLER,L.ANSELM,R.ECABERT,M.STIHLE, JRNL AUTH 2 B.GSELL,R.THOMA,J.DIEZ,J.M.BENZ,J.PLANCHER,G.HARTMANN, JRNL AUTH 3 Y.ISSHIKI,K.MORIKAMI,N.SHIMMA,W.HAAP,D.W.BANNER,F.DIEDERICH JRNL TITL HALOGEN BONDING AT THE ACTIVE SITES OF HUMAN CATHEPSIN L AND JRNL TITL 2 MEK1 KINASE: EFFICIENT INTERACTIONS IN DIFFERENT JRNL TITL 3 ENVIRONMENTS. JRNL REF CHEMMEDCHEM V. 6 2048 2011 JRNL REFN ISSN 1860-7179 JRNL PMID 21898833 JRNL DOI 10.1002/CMDC.201100353 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0112 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.78 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 45543 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.143 REMARK 3 R VALUE (WORKING SET) : 0.141 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2417 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2964 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.02 REMARK 3 BIN R VALUE (WORKING SET) : 0.3260 REMARK 3 BIN FREE R VALUE SET COUNT : 137 REMARK 3 BIN FREE R VALUE : 0.3180 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1688 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 271 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.88 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.02000 REMARK 3 B22 (A**2) : -1.15000 REMARK 3 B33 (A**2) : 2.18000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.053 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.052 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.048 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.766 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.982 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.972 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1897 ; 0.011 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 1269 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2589 ; 1.414 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3097 ; 0.889 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 242 ; 5.584 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 92 ;35.595 ;25.217 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 300 ;12.362 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;13.137 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 255 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2213 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 398 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 3166 ; 2.738 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 74 ;39.661 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3302 ;17.631 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. HYDROGENS GENERATED IN REFMAC, THOSE WITH ZERO REMARK 3 OCCUPANCY REMOVED. U VALUES REFINED INDIVIDUALLY. REMARK 4 REMARK 4 2YJ8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-MAY-11. REMARK 100 THE DEPOSITION ID IS D_1290048337. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-FEB-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.7 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50228 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.590 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.78000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.460 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: ISOMORPHOUS TO PDB ENTRY 2YJ2 REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 5.5, 0.2M SODIUM REMARK 280 ACETATE, 25 % PEG 3350 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 22.98750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.10900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.63250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.10900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.98750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.63250 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLU A 176 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLN A 21 50.96 -92.88 REMARK 500 GLN A 21 50.52 -92.66 REMARK 500 ASP A 160 70.73 -109.11 REMARK 500 ASP A 162 15.70 -140.09 REMARK 500 ALA A 202 127.95 -30.28 REMARK 500 ALA A 214 61.36 -151.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2008 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A2027 DISTANCE = 6.56 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE NITRILE (2S,4R)-4-(2-CHLORO-BENZENESULFONYL)-1-[1-(4-IODO-PHENYL REMARK 600 -CYCLOPROPANECARBONYL]-PYRROLIDINE-2-CARBOXYLIC ACID (1-CYANO- REMARK 600 CYCLOPROPYL)-AMIDE MAKES A COVALENT LINK TO THE ENZYME REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE YJ8 A 1221 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1222 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CJL RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A CYSTEINE PROTEASE PROFORM REMARK 900 RELATED ID: 1CS8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PROCATHEPSIN L REMARK 900 RELATED ID: 2XU4 RELATED DB: PDB REMARK 900 CATHEPSIN L WITH A NITRILE INHIBITOR REMARK 900 RELATED ID: 2VHS RELATED DB: PDB REMARK 900 CATHSILICATEIN, A CHIMERA REMARK 900 RELATED ID: 1ICF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MHC CLASS II ASSOCIATED P41 II FRAGMENT IN REMARK 900 COMPLEX WITH CATHEPSIN L REMARK 900 RELATED ID: 2XU3 RELATED DB: PDB REMARK 900 CATHEPSIN L WITH A NITRILE INHIBITOR REMARK 900 RELATED ID: 1MHW RELATED DB: PDB REMARK 900 DESIGN OF NON-COVALENT INHIBITORS OF HUMAN CATHEPSIN L .FROM THE 96- REMARK 900 RESIDUE PROREGION TO OPTIMIZED TRIPEPTIDES REMARK 900 RELATED ID: 2XU5 RELATED DB: PDB REMARK 900 CATHEPSIN L WITH A NITRILE INHIBITOR REMARK 900 RELATED ID: 2XU1 RELATED DB: PDB REMARK 900 CATHEPSIN L WITH A NITRILE INHIBITOR REMARK 900 RELATED ID: 2YJ9 RELATED DB: PDB REMARK 900 CATHEPSIN L WITH A NITRILE INHIBITOR REMARK 900 RELATED ID: 2YJB RELATED DB: PDB REMARK 900 CATHEPSIN L WITH A NITRILE INHIBITOR REMARK 900 RELATED ID: 2YJ2 RELATED DB: PDB REMARK 900 CATHEPSIN L WITH A NITRILE INHIBITOR REMARK 900 RELATED ID: 2YJC RELATED DB: PDB REMARK 900 CATHEPSIN L WITH A NITRILE INHIBITOR DBREF 2YJ8 A 1 220 UNP P07711 CATL1_HUMAN 114 333 SEQRES 1 A 220 ALA PRO ARG SER VAL ASP TRP ARG GLU LYS GLY TYR VAL SEQRES 2 A 220 THR PRO VAL LYS ASN GLN GLY GLN CYS GLY SER CYS TRP SEQRES 3 A 220 ALA PHE SER ALA THR GLY ALA LEU GLU GLY GLN MET PHE SEQRES 4 A 220 ARG LYS THR GLY ARG LEU ILE SER LEU SER GLU GLN ASN SEQRES 5 A 220 LEU VAL ASP CYS SER GLY PRO GLN GLY ASN GLU GLY CYS SEQRES 6 A 220 ASN GLY GLY LEU MET ASP TYR ALA PHE GLN TYR VAL GLN SEQRES 7 A 220 ASP ASN GLY GLY LEU ASP SER GLU GLU SER TYR PRO TYR SEQRES 8 A 220 GLU ALA THR GLU GLU SER CYS LYS TYR ASN PRO LYS TYR SEQRES 9 A 220 SER VAL ALA ASN ASP THR GLY PHE VAL ASP ILE PRO LYS SEQRES 10 A 220 GLN GLU LYS ALA LEU MET LYS ALA VAL ALA THR VAL GLY SEQRES 11 A 220 PRO ILE SER VAL ALA ILE ASP ALA GLY HIS GLU SER PHE SEQRES 12 A 220 LEU PHE TYR LYS GLU GLY ILE TYR PHE GLU PRO ASP CYS SEQRES 13 A 220 SER SER GLU ASP MET ASP HIS GLY VAL LEU VAL VAL GLY SEQRES 14 A 220 TYR GLY PHE GLU SER THR GLU SER ASP ASN ASN LYS TYR SEQRES 15 A 220 TRP LEU VAL LYS ASN SER TRP GLY GLU GLU TRP GLY MET SEQRES 16 A 220 GLY GLY TYR VAL LYS MET ALA LYS ASP ARG ARG ASN HIS SEQRES 17 A 220 CYS GLY ILE ALA SER ALA ALA SER TYR PRO THR VAL HET YJ8 A1221 58 HET GOL A1222 12 HETNAM YJ8 (2S,4R)-4-(2-CHLOROPHENYL)SULFONYL-N-[1-(IMINOMETHYL) HETNAM 2 YJ8 CYCLOPROPYL]-1-[1-(4-IODOPHENYL)CYCLOPROPYL]CARBONYL- HETNAM 3 YJ8 PYRROLIDINE-2-CARBOXAMIDE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 YJ8 C25 H25 CL I N3 O4 S FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *271(H2 O) HELIX 1 1 ARG A 8 GLY A 11 5 4 HELIX 2 2 SER A 24 GLY A 43 1 20 HELIX 3 3 SER A 49 SER A 57 1 9 HELIX 4 4 GLU A 63 CYS A 65 5 3 HELIX 5 5 LEU A 69 GLY A 81 1 13 HELIX 6 6 ASN A 101 LYS A 103 5 3 HELIX 7 7 GLN A 118 GLY A 130 1 13 HELIX 8 8 HIS A 140 PHE A 145 1 6 HELIX 9 9 ASN A 207 ILE A 211 5 5 SHEET 1 AA 2 VAL A 5 ASP A 6 0 SHEET 2 AA 2 HIS A 163 PHE A 172 1 O TYR A 170 N VAL A 5 SHEET 1 AB 2 ILE A 132 ILE A 136 0 SHEET 2 AB 2 HIS A 163 PHE A 172 -1 O HIS A 163 N ILE A 136 SHEET 1 AC 5 ILE A 150 TYR A 151 0 SHEET 2 AC 5 TYR A 198 ALA A 202 1 O LYS A 200 N TYR A 151 SHEET 3 AC 5 LYS A 181 LYS A 186 -1 O TRP A 183 N MET A 201 SHEET 4 AC 5 HIS A 163 PHE A 172 -1 O LEU A 166 N LYS A 186 SHEET 5 AC 5 ILE A 132 ILE A 136 -1 O ILE A 132 N VAL A 167 SHEET 1 AD 5 ILE A 150 TYR A 151 0 SHEET 2 AD 5 TYR A 198 ALA A 202 1 O LYS A 200 N TYR A 151 SHEET 3 AD 5 LYS A 181 LYS A 186 -1 O TRP A 183 N MET A 201 SHEET 4 AD 5 HIS A 163 PHE A 172 -1 O LEU A 166 N LYS A 186 SHEET 5 AD 5 VAL A 5 ASP A 6 1 O VAL A 5 N TYR A 170 SHEET 1 AE 2 LEU A 83 ASP A 84 0 SHEET 2 AE 2 SER A 105 ALA A 107 -1 N VAL A 106 O LEU A 83 SHEET 1 AF 2 GLY A 111 ASP A 114 0 SHEET 2 AF 2 SER A 216 THR A 219 -1 O TYR A 217 N VAL A 113 SSBOND 1 CYS A 22 CYS A 65 1555 1555 2.04 SSBOND 2 CYS A 56 CYS A 98 1555 1555 2.08 SSBOND 3 CYS A 156 CYS A 209 1555 1555 2.04 LINK SG CYS A 25 C18 YJ8 A1221 1555 1555 1.78 SITE 1 AC1 19 GLN A 19 GLY A 23 SER A 24 CYS A 25 SITE 2 AC1 19 TRP A 26 GLY A 61 GLY A 67 GLY A 68 SITE 3 AC1 19 LEU A 69 MET A 70 ALA A 135 MET A 161 SITE 4 AC1 19 ASP A 162 HIS A 163 GLY A 164 ARG A 206 SITE 5 AC1 19 ALA A 214 HOH A2131 HOH A2271 SITE 1 AC2 2 ASN A 18 HOH A2064 CRYST1 45.975 57.265 76.218 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.021751 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017463 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013120 0.00000